LC-1704-T_1
De novo transcriptome analysis was then performed. Clean data were produced by removing low-quality reads and adaptor sequences with fastp (https://github.com/OpenGene/fastp). To generate the transcriptome reference sequence, clean data for the 18 samples were merged for assembly with Trinity (https://github.com/trinityrnaseq/trinityrnaseq). TransRate (https://github.com/Blahah/ transrate) and CD-HIT (https://github.com/weizhongli/cdhit) were used for quality filtering. BUSCO (https://gitlab.com/ezlab/busco/-/releases#5.2.1) was used to assess the reference transcriptome assemblies. Clean reads from each L. chinensis sample were separately mapped against the reference transcriptome. Genes and transcripts were functionally annotated with the Gene Ontology (GO; geneontology.org), Kyoto Encyclopedia of Genes and Genomes (KEGG; https://www.genome.jp/kegg/), Clusters of Orthologous Groups (COG; https://www.ncbi.nlm.nih.gov/research/cog-project/), non-redundant protein (NR; https://www.ncbi.nlm.nih.gov/refseq/about/nonredundantproteins/), Swiss-Prot (https://www.expasy.org/resources/uniprotkb-swiss-prot), and Pfam (https://www.uniprot.org/database/DB-0073) databases.